Bottom Line:
By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels.However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology.In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations.

ABSTRACTEnvironmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.

fig01: Real-life and ideal fluxes of analysis and information in environmental genomics. Current throughputs of analysis and information-processing are given as black arrows, whereas the ideal throughputs to be achieved are shown as white arrows. Arrow thickness reflects the efficiency of the analyses.

Mentions:
This review is focussed on environmental genomics and post-genomics in an ecological context, where analyses of large-scale sequence information can reveal how functions and signals are propagated and integrated at the different ecological levels – individual, population, community, ecosystem – and across various temporal and spatial scales. The aim of environmental genomics, transcriptomics and proteomics in an ecological context is to understand the ecosystem ‘dark matter’ (Marcy et al. 2007) after translation into nucleic acid and protein sequences (Fig. 1; Box S1), by taking advantage of the fact that these sequences convey functional information, interact with ecosystem parameters through environmental signalling and acclimation processes, and have been shaped by evolutionary pressures, thus offering a glimpse of past environments.

fig01: Real-life and ideal fluxes of analysis and information in environmental genomics. Current throughputs of analysis and information-processing are given as black arrows, whereas the ideal throughputs to be achieved are shown as white arrows. Arrow thickness reflects the efficiency of the analyses.

Mentions:
This review is focussed on environmental genomics and post-genomics in an ecological context, where analyses of large-scale sequence information can reveal how functions and signals are propagated and integrated at the different ecological levels – individual, population, community, ecosystem – and across various temporal and spatial scales. The aim of environmental genomics, transcriptomics and proteomics in an ecological context is to understand the ecosystem ‘dark matter’ (Marcy et al. 2007) after translation into nucleic acid and protein sequences (Fig. 1; Box S1), by taking advantage of the fact that these sequences convey functional information, interact with ecosystem parameters through environmental signalling and acclimation processes, and have been shaped by evolutionary pressures, thus offering a glimpse of past environments.

Bottom Line:
By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels.However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology.In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations.

ABSTRACTEnvironmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism-environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.